Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans

Abstract

BackgroundWhile a few studies on the variations in mRNA expression and half-lives measured under different growth conditions have been used to predict patterns of regulation in bacterial organisms, the extent to which this information can also play a role in defining metabolic phenotypes has yet to be examined systematically. Here we present the first comprehensive study for a model methanogen.ResultsWe use expression and half-life data for the methanogen Methanosarcina acetivorans growing on fast- and slow-growth substrates to examine the regulation of its genes. Unlike Escherichia coli where only small shifts in half-lives were observed, we found that most mRNA have significantly longer half-lives for slow growth on acetate compared to fast growth on methanol or trimethylamine. Interestingly, half-life shifts are not uniform across functional classes of enzymes, suggesting the existence of a selective stabilization mechanism for mRNAs. Using the transcriptomics data we determined whether transcription or degradation rate controls the change in transcript abundance. Degradation was found to control abundance for about half of the metabolic genes underscoring its role in regulating metabolism. Genes involved in half of the metabolic reactions were found to be differentially expressed among the substrates suggesting the existence of drastically different metabolic phenotypes that extend beyond just the methanogenesis pathways. By integrating expression data with an updated metabolic model of the organism (iST807) significant differences in pathway flux and production of metabolites were predicted for the three growth substrates.ConclusionsThis study provides the first global picture of differential expression and half-lives for a class II methanogen, as well as provides the first evidence in a single organism that drastic genome-wide shifts in RNA half-lives can be modulated by growth substrate. We determined which genes in each metabolic pathway control the flux and classified them as regulated by transcription (e.g. transcription factor) or degradation (e.g. post-transcriptional modification). We found that more than half of genes in metabolism were controlled by degradation. Our results suggest that M. acetivorans employs extensive post-transcriptional regulation to optimize key metabolic steps, and more generally that degradation could play a much greater role in optimizing an organism’s metabolism than previously thought.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3219-8) contains supplementary material, which is available to authorized users.

meCLICK-Seq, a Substrate-Hijacking and RNA Degradation Strategy for the Study of RNA Methylation

“…Although the kinetic profile of RNA degradation may be complex, first-order half-lives are often used as an estimate of RNA stability. 21 By using a first-order approximation, we have calculated the functionalized RNA 11-mer to have a half-life of 2.6 h ( Figure S1d ). Additionally, we carried out the click-degrader functionalization and degradation on two longer oligomers ( Figure S2a–c ).…”

Short-Term Exposure of Paddy Soil Microbial Communities to Salt Stress Triggers Different Transcriptional Responses of Key Taxonomic Groups

“…There was a nearly exact correspondence between the stress-induced decrease in net acetate consumption, methane production, and the proportion of mRNA in total RNA [∼50% (300 mM NaCl) and 65–70% (600 mM NaCl)]. Obviously, mRNA turnover is more responsive to environmental change and adverse conditions than rRNA dynamics, in good correspondence to the mRNA half-lives that are known to be for bacteria in the order of minutes and for methanogenic archaea in the range of tens of minutes and a few hours (Evguenieva-Hackenberg and Klug, 2009; Peterson et al, 2016). The strong decrease in functional gene expression, however, was related to tremendous changes in the taxonomic and functional profiles of enriched mRNA.…”

Current status and applications of genome-scale metabolic models

“…GEM reconstruction studies have mainly focused on prokaryotes and eukaryotes, but GEMs have also been built for a few archaea, such as Methanosarcina acetivorans , a methanogenic archaeal species which lives in a marine environment [40–43]. GEMs of M. acetivorans contain information on the methanogenesis pathway, the most representative metabolism of methanogens [44].…”

“…iMAC868 was curated to represent a thermodynamically feasible methanogenesis reversal pathway that co-utilizes methane and bicarbonate, among other updates made in the GEM [42]. Another recent GEM of M. acetivorans , iST807 [43], was also updated on the basis of the previous version, iMB745 [41], in order to consider the effects of regulators on metabolic pathways in media containing different substrates. For example, in addition to the newly added metabolic pathways, tRNA-charging was explicitly incorporated into iST807, thereby allowing characterization of the effects of the differential expression of tRNA genes on metabolic fluxes.…”